Understanding the influence of SiC reaction with CO, a by-product of SiC thermal oxidation, is a key point to elucidate the origin of electrical defects in SiC metal-oxide-semiconductor (MOS) devices. In this work, the effects on electrical, structural, and chemical properties of SiO2/Si and SiO2/SiC structures submitted to CO annealing were investigated. It was observed that long annealing times resulted in the incorporation of carbon from CO in the Si substrate, followed by deterioration of the SiO2/Si interface, and its crystallization as SiC. Besides, this incorporated carbon remained in the Si surface (previous SiO2/Si region) after removal of the silicon dioxide film by HF etching. In the SiC case, an even more defective surface region was observed due to the CO interaction. All MOS capacitors formed using both semiconductor materials presented higher leakage current and generation of positive effective charge after CO annealings. Such results suggest that the negative fixed charge, typically observed in SiO2/SiC structures, is not originated from the interaction of the CO by-product, formed during SiCoxidation, with the SiO2/SiC interfacial region.